New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
2 years
267
11
92093
5872
0
91
Parser of scientific names (...) !
Dmitry Mozzherin
2 weeks
19
4
50275
4771
2
17
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
1 week
6
2
42272
2584
0
14
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
12 months
14
11
38688
2357
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
3 months
19
6
38619
4751
0
9
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
3 months
2
...
29963
1880
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
14 months
13
1
25381
1766
0
0
Gadgets for bioinformatics (...)
Shintaro Katayama
23 months
1
25337
2608
Http requests to entrez e-utilities (...)
Jared Ning
5 weeks
4
...
24373
1535
0
3
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
1 week
24058
4363
A Ruby api for interacting with biomart services (...) !
Darren Oakley
3 years
17
5
23281
1075
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
14 months
22803
1203
Create pretty svg-format images of features, gene models (...)
Dan MacLean
16 months
10
5
21052
3411
0
0
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
18964
1056
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
31
18283
1315
0
0
Interfaces with biomodel search engine (...) !
Niall Beard
3 years
1
...
16106
875
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
15903
1224
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
3 weeks
12
1
15230
1672
0
5
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
3 years
4
2
15146
890
A simple obo file handler (...) !
mjy
3 years
4
...
14086
755
A fast parser for fastq files (...)
Francesco Strozzi
2 years
10
...
11388
777
0
0
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
12 months
8
5
11183
755
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
12 months
9
20
11169
946
0
0
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
4 months
12
2
11164
1498
Data mining algorithms for jRuby (...)
arrigonialberto86
20 months
14
3
9939
1140
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
2 years
1
...
9591
622
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
2
1
9454
518
Low memory sequence emitters (...)
Pjotr Prins
12 months
8
1
9175
636
A nexus file format (phylogenetic inference) parser in (...) !
mjy
4 years
1
...
8962
433
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
9 months
3
...
8626
641
0
0
Build genome output files (...)
Michael Barton
21 months
5
...
8498
405
Ruby support for the baclava file format (...) !
Robert Haines
15 months
1
...
8473
518
0
0
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
2 weeks
2
2
8305
2484
0
11
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
8239
422
0
0
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
8062
374
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
8021
516
0
0
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
24 months
5
...
7810
605
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
23 months
8
...
7790
413
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
3 years
7
2
7752
429
0
0
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
7692
521
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
14 months
...
7588
474
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
3 years
3
...
7567
432
0
0
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
7516
311
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
6994
321
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
4 years
4
...
6885
327
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
30
14
6667
399
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
4 years
1
...
6270
312
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
6009
451
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
21 months
12
2
5778
716
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
4 years
4
...
5600
327
0
0
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
10
...
5463
240
0
0
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
5380
311
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
2 years
2
1
5215
417
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
5185
315
Taverna player is a rails plugin to run (...)
Robert Haines
3 months
4
3
5135
825
0
6
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
39
5
4963
195
0
0
Ruby binding for samtools tabix (...)
throwern
20 months
3
...
4938
402
0
0
Parser to work with file formats used in (...)
Ben J Woodcroft
4 months
...
4485
859
0
0
Fast multi-threaded vcf parser (...)
Pjotr Prins
5 months
18
7
4426
921
0
4
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
4360
308
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
4309
313
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
4284
316
0
0
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
4271
305
0
0
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
4208
216
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
4174
217
Bioinformatics triple-store support (...)
Pjotr Prins
3 years
4
1
3956
233
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
3918
230
0
0
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
12 weeks
...
3739
1204
0
5
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
20 months
3705
386
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3637
202
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
2 years
3487
296
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
3 years
2
...
3478
214
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3423
205
0
0
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
2 years
...
3392
320
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
21 months
1
...
3375
315
Parse pfam hmm definition files (...)
Ben J. Woodcroft
3 years
1
...
3094
211
0
0
Rocker (...)
Luis (Coto) Orellana, Luis M. Rodriguez-R
3 weeks
3039
2669
A protparam compatible utility for BioRuby (...)
hryk
2 years
2
...
3024
206
0
0
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
2929
207
Publish scientific results to the semantic web (...) !
Will Strinz
11 months
3
16
2768
319
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
14 months
1
...
2569
408
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
4 months
1
2331
592
0
0
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2173
106
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
2169
108
A general purpose framework for scripted handling of (...) development/stable
mjy
2 years
2
1
2169
541
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
2162
105
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
5 years
1
...
2074
87
0
0
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
6 months
1
2055
648
0
0
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
15 months
6
...
2045
127
Gggenome Ruby client (...)
Mitsuteru Nakao
21 months
1
...
1946
209
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
4 years
1
...
1912
113
Biostars data-mining and statistical analysis (...)
Joachim Baran
13 months
1892
311
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1884
96
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1874
109
Ruby ensembl rest api (...)
Alberto Donizetti
20 months
3
...
1862
206
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1861
98
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
1
...
1854
421
0
0
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1847
105
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1833
102
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1822
106
Generalized linear models for statsample (...)
Ankur Goel
20 months
1814
211
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
3 years
3
...
1796
103
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1787
107
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1756
105
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1749
103
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
3 years
1
1
1668
109
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
16 months
...
1572
224
Build graph with jRuby (...)
Matteo Picciolini
2 years
1564
105
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
3
...
1557
111
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
16 months
...
1547
214
Bio-repeatmasker (...)
Andrei Rozanski
16 months
1513
204
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
6 years
5
...
1472
291
0
0
A parser for cigar format alignments (...)
Ben J Woodcroft
15 months
4
...
1404
229
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1309
108
Web server for bio-samtools (...)
homonecloco
12 months
...
1260
230
0
0
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
23 months
2
...
1101
113
0
0
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
7 months
1046
219
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
22 months
...
1033
107
0
0
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
89
1
746
143
0
0
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
5 months
1
...
739
243
0
0
Mine publications for gene names (...)
Pjotr Prins
15 months
...
703
105
Helper methods for reading .delta files (...)
robsyme
8 weeks
...
653
513
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
14 months
623
83
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
10 months
1
...
556
111
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
8 months
...
517
124
0
0
Tools to work with fasta files, indexed with (...)
homonecloco
7 months
...
474
115
Tools to manipulate blat files from the command (...)
homonecloco
7 months
...
459
107
(...) pre
pre
420
25
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
6 months
...
417
119
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
6 months
...
417
126
0
0
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
386
77
!
The api for freebayes version #{bio::freebayes::extversion} (...) new
Natapol Pornputtapong
6 days
273
241
!
Api of picard tool (...) new
Natapol Pornputtapong
1 week
254
133
A web app wrapper for genevalidator (...) !
Ismail Moghul
6 days
...
232
232
0
19
Bioinformatics. aggregate fastqc (quality control for next generation (...)
Raoul Jean Pierre Bonnal
9 weeks
...
225
225
A pipeline manager (...)
Francesco Strozzi
9 weeks
8
10
209
209
(...) pre
pre
175
35
Identifying problems with gene predictions (...) !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
6 days
142
142
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-05-28
**) number of commits on GitHub (last 7 days & last 90 days)